Exploring the " dark matter" of a mammalian proteome by protein structure and function modeling

Proteome Science

Volumn 11, Issue 1, 2013, Pages

  Brylinski, Michal ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ALGORITHM; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; GENOME; LIGAND BINDING; METAL BINDING; MOUSE; NONHUMAN; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; QUALITY CONTROL; STRUCTURAL BIOINFORMATICS;

MAMMALIA;

EID: 84889854589     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-11-47     Document Type: Article

References (77)

1. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113. 10.1038/nrg1272, 14735121.
2. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
3. Ng PC, Kirkness EF. Whole genome sequencing. Methods Mol Biol 2010, 628:215-226. 10.1007/978-1-60327-367-1_12, 20238084.
4. Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 2011, 6:e17288. 10.1371/journal.pone.0017288, 3052304, 21408061.
5. Zhou Q, Su X, Wang A, Xu J, Ning K. QC-Chain: fast and holistic quality control method for next-generation sequencing data. PLoS One 2013, 8:e60234. 10.1371/journal.pone.0060234, 3615005, 23565205.
6. Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods 2011, 8:61-65. 10.1038/nmeth.1527, 3115693, 21102452.
7. Das S, Yu L, Gaitatzes C, Rogers R, Freeman J, Bienkowska J, Adams RM, Smith TF, Lindelien J. Biology's new Rosetta stone. Nature 1997, 385:29-30. 10.1038/385029a0, 8985242.
8. Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A. On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 2001, 17:425-428. 10.1016/S0168-9525(01)02372-1, 11485798.
9. Ochman H. Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet 2002, 18:335-337. 10.1016/S0168-9525(02)02668-9, 12127765.
10. Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, et al. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet 2006, 2:e62. 10.1371/journal.pgen.0020062, 1449903, 16683036.
11. The UniProt Consortium The Universal Protein resource (UniProt). Nucleic Acids Res 2007, 35:193-197. 1802568, 17158163, The UniProt Consortium.
12. Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM. The abundance of short proteins in the mammalian proteome. PLoS Genet 2006, 2:e52. 10.1371/journal.pgen.0020052, 1449894, 16683031.
13. Hobbs EC, Fontaine F, Yin X, Storz G. An expanding universe of small proteins. Curr Opin Microbiol 2011, 14:167-173. 10.1016/j.mib.2011.01.007, 3079058, 21342783.
14. Handler AA, Lim JE, Losick R. Peptide inhibitor of cytokinesis during sporulation in Bacillus subtilis. Mol Microbiol 2008, 68:588-599. 10.1111/j.1365-2958.2008.06173.x, 2603569, 18284588.
15. Ramamurthi KS, Lecuyer S, Stone HA, Losick R. Geometric cue for protein localization in a bacterium. Science 2009, 323:1354-1357. 10.1126/science.1169218, 2652684, 19265022.
16. Waters LS, Sandoval M, Storz G. The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. J Bacteriol 2011, 193:5887-5897. 10.1128/JB.05872-11, 3194919, 21908668.
17. Gassel M, Mollenkamp T, Puppe W, Altendorf K. The KdpF subunit is part of the K(+)-translocating Kdp complex of Escherichia coli and is responsible for stabilization of the complex in vitro. J Biol Chem 1999, 274:37901-37907. 10.1074/jbc.274.53.37901, 10608856.
18. Guillen G, Diaz-Camino C, Loyola-Torres CA, Aparicio-Fabre R, Hernandez-Lopez A, Diaz-Sanchez M, Sanchez F. Detailed analysis of putative genes encoding small proteins in legume genomes. Front Plant Sci 2013, 4:208. 3687714, 23802007.
19. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
20. Yang X, Tschaplinski TJ, Hurst GB, Jawdy S, Abraham PE, Lankford PK, Adams RM, Shah MB, Hettich RL, Lindquist E, et al. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res 2011, 21:634-641. 10.1101/gr.109280.110, 3065711, 21367939.
21. Mulder N, Apweiler R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 2007, 396:59-70. 10.1007/978-1-59745-515-2_5, 18025686.
22. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
23. Ladoukakis E, Pereira V, Magny EG, Eyre-Walker A, Couso JP. Hundreds of putatively functional small open reading frames in Drosophila. Genome Biol 2011, 12:R118. 10.1186/gb-2011-12-11-r118, 3334604, 22118156.
24. Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A. Protein function annotation by homology-based inference. Genome Biol 2009, 10:207. 10.1186/gb-2009-10-2-207, 2688287, 19226439.
25. Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y. Automatic prediction of protein function. Cell Mol Life Sci 2003, 60:2637-2650. 10.1007/s00018-003-3114-8, 14685688.
26. Abascal F, Valencia A. Automatic annotation of protein function based on family identification. Proteins 2003, 53:683-692. 10.1002/prot.10449, 14579359.
27. Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biol 2009, 10:206. 10.1186/gb-2009-10-2-206, 2688272, 19226438.
28. Bork P, Koonin EV. Predicting functions from protein sequences-where are the bottlenecks?. Nat Genet 1998, 18:313-318. 10.1038/ng0498-313, 9537411.
29. Ponting CP. Issues in predicting protein function from sequence. Brief Bioinform 2001, 2:19-29. 10.1093/bib/2.1.19, 11465059.
30. Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 2002, 18:1641-1649. 10.1093/bioinformatics/18.12.1641, 12490449.
31. Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 2009, 5:e1000605. 10.1371/journal.pcbi.1000605, 2781113, 20011109.
32. Kim SH, Shin DH, Choi IG, Schulze-Gahmen U, Chen S, Kim R. Structure-based functional inference in structural genomics. J Struct Funct Genomics 2003, 4:129-135. 10.1023/A:1026200610644, 14649297.
33. Dey F, Cliff Zhang Q, Petrey D, Honig B. Toward a "structural BLAST": using structural relationships to infer function. Protein Sci 2013, 22:359-366. 10.1002/pro.2225, 23349097.
34. Brylinski M, Skolnick J. Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins 2010, 78:118-134. 2804779, 19731377.
35. Skolnick J, Brylinski M. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 2009, 10:378-391. 10.1093/bib/bbp017, 2691936, 19324930.
36. Brylinski M. Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 2013, 4:118. 3686302, 23802014.
37. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997, 5:1093-1108. 10.1016/S0969-2126(97)00260-8, 9309224.
38. Brylinski M, Feinstein WP. Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 2012, 6:001-010.
39. Brylinski M, Lingam D. eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS One 2012, 7:e50200. 10.1371/journal.pone.0050200, 3503980, 23185577.
40. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57:702-710. 10.1002/prot.20264, 15476259.
41. Maiorov VN, Crippen GM. Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. J Mol Biol 1994, 235:625-634. 10.1006/jmbi.1994.1017, 8289285.
42. Wang Z, Eickholt J, Cheng J. APOLLO: a quality assessment service for single and multiple protein models. Bioinformatics 2011, 27:1715-1716. 10.1093/bioinformatics/btr268, 3106203, 21546397.
43. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993, 26:283-291.
44. Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006, 34:3698-3707. 10.1093/nar/gkl454, 1540721, 16893954.
45. Jochim AL, Arora PS. Assessment of helical interfaces in protein-protein interactions. Mol Biosyst 2009, 5:924-926. 10.1039/b903202a, 19668855.
46. Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995, 63:31-65. 10.1016/0079-6107(94)00008-W, 7746868.
47. Mangelsdorf DJ, Thummel C, Beato M, Herrlich P, Schutz G, Umesono K, Blumberg B, Kastner P, Mark M, Chambon P, et al. The nuclear receptor superfamily: the second decade. Cell 1995, 83:835-839. 10.1016/0092-8674(95)90199-X, 8521507.
48. Novac N, Heinzel T. Nuclear receptors: overview and classification. Curr Drug Targets Inflamm Allergy 2004, 3:335-346. 10.2174/1568010042634541, 15584884.
49. McKenna NJ, Lanz RB, OMalley BW. Nuclear receptor coregulators: cellular and molecular biology. Endocr Rev 1999, 20:321-344. 10.1210/er.20.3.321, 10368774.
50. Aranda A, Pascual A. Nuclear hormone receptors and gene expression. Physiol Rev 2001, 81:1269-1304.
51. Brylinski M, Feinstein WP. eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 2013, 27:551-567. 10.1007/s10822-013-9663-5, 23838840.
52. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
53. Luenser K, Ludwig A. Variability and evolution of bovine beta-defensin genes. Genes Immun 2005, 6:115-122. 10.1038/sj.gene.6364153, 15674371.
54. Brylinski M, Skolnick J. FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins 2011, 79:735-751. 10.1002/prot.22913, 3060289, 21287609.
55. Andreini C, Bertini I, Rosato A. Metalloproteomes: a bioinformatic approach. Acc Chem Res 2009, 42:1471-1479. 10.1021/ar900015x, 19697929.
56. Dokmanic I, Sikic M, Tomic S. Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination. Acta Crystallogr D Biol Crystallogr 2008, 64:257-263. 10.1107/S090744490706595X, 18323620.
57. Harding MM. The architecture of metal coordination groups in proteins. Acta Crystallogr D Biol Crystallogr 2004, 60:849-859. 10.1107/S0907444904004081, 15103130.
58. Passerini A, Punta M, Ceroni A, Rost B, Frasconi P. Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 2006, 65:305-316. 10.1002/prot.21135, 16927295.
59. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
60. Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 2003, 326:317-336. 10.1016/S0022-2836(02)01371-2, 12547212.
61. Biegert A, Soding J. Sequence context-specific profiles for homology searching. Proc Natl Acad Sci U S A 2009, 106:3770-3775. 10.1073/pnas.0810767106, 2645910, 19234132.
62. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960. 10.1093/bioinformatics/bti125, 15531603.
63. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011, 39:W29-37. 10.1093/nar/gkr367, 3125773, 21593126.
64. Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 2002, 3:265-274. 10.1093/bib/3.3.265, 12230035.
65. Lobley A, Sadowski MI, Jones DT. pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics 2009, 25:1761-1767. 10.1093/bioinformatics/btp302, 19429599.
66. Hughey R, Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 1996, 12:95-107.
67. Zhou H, Zhou Y. SPARKS 2 and SP3 servers in CASP6. Proteins 2005, 61(Suppl 7):152-156.
68. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992, 358:86-89. 10.1038/358086a0, 1614539.
69. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234:779-815. 10.1006/jmbi.1993.1626, 8254673.
70. Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995, 23:566-579. 10.1002/prot.340230412, 8749853.
71. McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994, 238:777-793. 10.1006/jmbi.1994.1334, 8182748.
72. Pandit SB, Skolnick J. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinforma 2008, 9:531.
73. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. Ensembl 2011. Nucleic Acids Res 2011, 39:D800-806. 10.1093/nar/gkq1064, 3013672, 21045057.
74. Tobi D, Bahar I. Optimal design of protein docking potentials: efficiency and limitations. Proteins 2006, 62:970-981.
75. Brylinski M, Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A 2008, 105:129-134. 10.1073/pnas.0707684105, 2224172, 18165317.
76. Tanimoto TT. An elementary mathematical theory of classification and prediction. IBM Internal Report 1958, New York.
77. Irwin JJ, Shoichet BK. ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 2005, 45:177-182. 10.1021/ci049714+, 1360656, 15667143.